What happened is the request you sent to the CA (in this case godaddy) did not come from the certificate that you are trying to match up with the signed certificate that godaddy sent you.
The short answer to your question/dilema is to just create a new request using the keytool, for example:
keytool -certreq -alias mydomain -keystore keystore.jks -file mydomain.csr
Then you should send this request to godaddy for reprocessing. They should not charge you again, as I believe it's their policy to do reissues free of charge. If both domains are on the same multidomain certificates, then you should not have to buy 2 seperate certs.